5-65093838-A-G

Variant names:

• chr5-65093838-A-G
• rs1117707
• ENST00000693303.1:c.1153-5414A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693303.1(CWC27):​c.1153-5414A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,876 control chromosomes in the GnomAD database, including 8,719 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (8719 hom., cov: 31)
• Consequence: CWC27 ENST00000693303.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 6 publications found

Genes affected

CWC27 (HGNC:10664): (CWC27 spliceosome associated cyclophilin) Predicted to enable peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in protein peptidyl-prolyl isomerization. Located in nucleoplasm. Part of U2-type precatalytic spliceosome and catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Apr 2022]

CWC27 Gene-Disease associations (from GenCC):

• metaphyseal chondrodysplasia-retinitis pigmentosa syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ENSG00000300368 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693303.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CWC27	ENST00000693303.1		c.1153-5414A>G		intron	N/A	ENSP00000508557.1
	ENSG00000300368	ENST00000771212.1		n.148+20328A>G		intron	N/A
	ENSG00000300404	ENST00000771409.1		n.74+4604T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50671 AN: 151758 Hom.: 8702 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.334 AC: 50720 AN: 151876 Hom.: 8719 Cov.: 31 AF XY: 0.334 AC XY: 24761 AN XY: 74226

African (AFR) AF: 0.347 AC: 14360 AN: 41396

American (AMR) AF: 0.404 AC: 6169 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1748 AN: 5148

South Asian (SAS) AF: 0.409 AC: 1962 AN: 4796

European-Finnish (FIN) AF: 0.291 AC: 3076 AN: 10556

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.313 AC: 21284 AN: 67932

Other (OTH) AF: 0.305 AC: 643 AN: 2110

Alfa AF: 0.196 Hom.: 395

Bravo AF: 0.338

Asia WGS AF: 0.377 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.29
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1117707; hg19: chr5-64389665;